Epigenetic and

Expression
Regulation
Sofia Mubarika

DNA

RNA

PROTEIN

Genome : 40.000 genes

Transcriptome > 100.000 RNA
Proteome > 400.000 proteins
Variability :
genomic variations
Gene expression,
alternative splicing
Protein
cleavage,modification

Central Dogma
DNA
Translation

RNA
Transcription
A gene is expressed in 3 steps:

Protein

1) Transcription: RNA synthesis

2) Splicing: removal of intron sequence from RNA
3) Translation: Protein synthesis

Central Dogma

DNA

Genotype
RNA function &
structure
Protein sequence

RNA

Protein structure

Protein

Protein Function
Phenotype

Gene Regulatory Mechanisms

Transcriptional Mechanisms
Type of promoters & RNA polymerase
Control of Transcription
Constitutive
Inducible
Repressible
Transcription Factors and TFBS
Translational Mechanisms
Micro RNAs (miRNAs and RITS complexes)
Translational control
mRNA degradation
Promoter activation
Silencer RNAs (siRNAs & RISC complexes) degrading mRNA
Epigenetic Mechanisms
Chromatin remodeling
Histone modifications (acetylation, phosphorylation,
methylation )
DNA methylation

Epigenetics ??
Epigenetics is:

Genome
DNA

Reversible changes in
gene expression
Without

changes in
DNA sequence

Can

be inherited
from precursor cells

Epigenetic information
is included in the
epigenome

Chromatin

Epigenome

Gene Expression

Phenotype

Chromatin Key Component of

Epigenetic Mechanisms
Cellular DNA is packaged into a structure called
chromatin
The unit of chromatin is the nucleosome, a complex
of a histone tetramer with approx. 125 bp of DNA
wound around it
nucleosome

histone
DNA

chromatin

Chromatin organizes genes to be accessible

for transcription, replication, and repair

DNA Methylation can Prevent Gene

Expression
DNMT

TF

DNMT
TF

Ac

Ac

Ac

Ac
Ac

Gene
expression

Ac

Ac

Ac

Ac Ac
Ac

DNMT

Ac

Me

Me
Ac

Me

DNMT
Me

Me
Ac

Ac

Ac

Me
Ac

Ac

Gene
expression

DNA methylation involves the transfer of methyl groups to

cytosine residues in DNA by DNA methyltransferases (DNMTs)

May prevent transcription factors from binding to DNA

May serve as binding site for methylated DNA-binding

proteins,
such as MECP2, which then recruit HDACs

Me

Histone Methylation can Affect

Chromatin Structure
Me

HDAC
HMT

Me

Me
Me

Ac

Ac

Me

Me

Me

HMT
HDAC

Ac

Me

Me

Gene
expression

Me

Gene
expression

Histone methylation by histone methyltransferases

(HMTs) can recruit HDACs, leading to:
Closed chromatin structure
Gene silencing

Other Epigenetic Modifications of

Histones and DNA
Histone
Methylation

Histone
Acetylation
Ac

Me Me
Me

DNA
Methylation

Epigenetic Modifications to Histones and DNA Can

Cooperate to Silence Gene Expression
DNMT

DNMT

HDAC

Ac
Ac
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Ac

Ac

Ac
Ac

Ac

Ac

Ac

Ac

Ac

Ac
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Ac

Ac

HDAC

TF
Me
Me

Me
Me

Me

Me

Me

Gene
expression

Epigenetic modifications can cooperate to silence gene expression

Imbalanced Levels of Histone

Acetylation Deregulate Gene
Expression
HAT

HISTONE
ACETYLATION

TF
Ac

Ac
Ac

TF

Deacetylated
Histones
Closed chromatin
Transcription factors
cannot access DNA

HISTONE
DEACETYLATION

HDAC

Ac

Ac
Ac

Ac
Ac

Ac

Acetylated
Histones
Open chromatin
Transcription factors
can access DNA

Increased HDAC activity or decreased HAT activity may result

in aberrant gene expression, contributing to cancer

Epigenetics Play Important Roles in Normal

Cellular Development and in Cancer
EPIGENETICS

Normal epigenetic
mechanisms

Normal differentiated cells, e.g.

embryonic cells, hematopoetic cells

Deregulated epigenetic
mechanisms

Malignant
progenitor cell

Tumor

Epigenetic mechanisms can regulate genes involved in

differentiation, cell cycle, and cell survival

Deregulation of epigenetic mechanisms results in aberrant gene

expression, which can lead to cancer

Reversal of deregulated epigenetic changes is a rational

strategy for targeting cancer

Historically, Cancer Was Considered to

be Driven Mostly by Genetic Changes
GENETIC

Example:
Replication errors
X X

Altered
DNA sequence
Altered
DNA/mRNA/proteins

Oncogenesis

Tumor

Epigenetic Changes Important in

Causing Cancer
GENETIC

EPIGENETIC

Example:
Chromatin modification errors

Example:
Replication errors
X X

Altered
chromatin structure

Altered
DNA sequence
Altered
DNA/mRNA/proteins

Oncogenesis

Tumor

Altered levels of
miRNA/proteins

Cancer epigenetics

Epigenetic alterations found in almost all

types of cancers
50% of genes that cause familial forms of
cancer are found silenced in sporadic forms of
cancer
Large number of epigenetic alterations found
in cancer cells due to:
Stochastic occurrences that accumulate with
age, selected for during tumour formation
Caused by defects in components of the
epigenetic machinery
Repair gene (repair defects) alterations

Cancer epigenetics

Changes in 5-me-C distribution in DNA

Hypermethylation of promoter CpG islands (found in
~50% genes) associated with TSGs
Decreased expression levels/silencing of TSGs
Increased mutations
Global hypomethylation
Chromosome instability (particularly pericentromeric
repeats)
Activation of viruses
Activation of proto-oncogene
Changes in chromatin structure
Histone modifications:
Histone deacetylation
Histone methylation (H3-K9); demethylation (H3-K4)
Histone sumoylation
Heterochromatin-associated proteins

Epigenetics & Genetic Mutations Can

Cooperate to Promote Oncogenesis
GENETIC

EPIGENETIC

Oncogene function

Oncogene levels

Tumor suppressor function

Tumor suppressor
levels
Oncogenesis

Tumor

Epigenetics Play Important Roles in

Normal & Cancer Development
EPIGENETICS

Normal epigenetic
mechanisms

Normal differentiated cells, e.g.

embryonic cells, hematopoetic cells

Deregulated epigenetic
mechanisms

Malignant
progenitor cell

Tumor

Epigenetic mechanisms can regulate genes involved in

differentiation, cell cycle, and cell survival

Deregulation of epigenetic mechanisms results in aberrant gene

expression, which can lead to cancer

Reversal of deregulated epigenetic changes is a rational

strategy for targeting cancer

Cancer Stem Cell Theory: the Root

of Cancer Growth

Tumor

Tumor
Development
and
Growth
Epigenetically
altered, self-renewing
cancer stem cells

Conventional Therapies May Target Tumor

Cells,
Not Cancer Stem Cells
Conventional
therapy

Target tumor

Cancer stem
cells survive

Tumor
regrowth

Epigenetic Therapy May Target Cancer Stem

Cells and Tumor Cells
Epigenetic
therapy

Target tumor
and cancer
stem cells

Tumor and
cancer stem
cell death

No
regrowth

Section 1: Importance of Epigenetics in Cancer

Section 2: Mechanisms of Epigenetics: Focus on

Deacetylation

Section 3: Therapeutic Targeting of Epigenetics

Basic Epigenetic Mechanisms: Post

Translational Modifications to Histones and
Base Changes in DNA

Epigenetic modifications of histones and DNA include:

Histone acetylation and methylation, and DNA methylation

Histone
Methylation

Histone
Acetylation
Ac

Me

Me Me

DNA Methylation

Histone Proteins in Chromatin Can be

Modified by Acetylation

Histone
Acetylation

Histone
Methylation
Ac

Me Me
Me

DNA Methylation

Epigenetic Changes can Alter

Chromatin Structure and Regulate
Gene Expression
TF

TF

Ac

Ac

Ac

Ac

Ac

Ac

Ac

Ac

Ac

Gene
expression

Gene
expression

Gene expression (transcription) requires DNA to be physically

accessible to transcription factors (TF)
Epigenetic changes alter the structure of the chromatin, which
determines whether DNA is accessible
Open chromatin allows gene expression
Closed chromatin prevents gene expression

In Cancer, Changes in Chromatin

Structure Can
Silence Tumor Suppressor Genes
Normal
cells

Ac

Ac

Ac

Ac

Ac
Ac

Cancer
cells

Ac
Ac

Ac

Tumor suppressor
gene expression

Tumor suppressor
gene expression

Silencing of tumor suppressor genes, a major process in

tumorigenesis, may result from epigenetic changes that
condense chromatin structure

Balance of Histone Acetylation is a Key

Factor in Transcriptional Regulation in
Normal Cells
HAT
HISTONE
ACETYLATION

TF

TF

Ac

Ac

Ac

Ac

Ac
Ac

Ac
Ac

Ac

Deacetylated
Histones

Acetylated
Histones

Closed chromatin
Transcription factors
cannot access DNA

Open chromatin
Transcription factors
can access DNA

Gene
expression

Gene
expression

Balance of Histone Acetylation is a Key

Factor in Transcriptional Regulation in
Normal Cells
HAT
HISTONE
ACETYLATION

TF

TF

Ac

Ac

Ac

Ac

Ac
Ac

Ac
Ac

Ac

HISTONE
DEACETYLATION

Deacetylated
Histones
Closed chromatin
Transcription factors
cannot access DNA
Gene
expression

HDAC
HDAC

Acetylated
Histones
Open chromatin
Transcription factors
can access DNA
Gene
expression

Section 1: Importance of Epigenetics in Cancer

Section 2: Mechanisms of Epigenetics: Focus on

Deacetylation

Section 3: Therapeutic Targeting of Epigenetics

Increased HDAC Activity Can Alter Gene

Expression and Result in Cancer

TF

HDAC

Increased HDAC activity

associated with certain
tumors, can alter expression
of genes involved in normal
cell development, resulting
in:

Loss of cell-cycle arrest

Inhibition of
differentiation

Cell growth and

proliferation

Evasion of apoptosis

Migration and metastasis

Gene expression

Cell nucleus

HDAC Inhibition Can Reverse

Altered Gene Expression

Inhibition of HDAC
activity can restore
the balance of
histone acetylation

Targeting HDAC
activity may
therefore allow
re-expression of
silenced genes to
reverse
oncogenesis

DAC
Inhibitor
HDAC

TF

Ac

Ac

Ac

Cell-cycle arrest
Differentiation

Gene
expression

Growth control
Apoptosis
Adhesion

Cell nucleus

Therapeutic Targeting of Both Histone and

DNA Modifications Can Synergize
DNMT
Inhibitor
DAC
Inhibitor

DNMT

HDAC

TF
Ac

Ac

Ac

Ac

Ac

Ac

Cell-cycle arrest
Differentiation

Gene
expression

Growth control
Apoptosis
Adhesion

Cell nucleus

Since DNA
methylation and
histone
deacetylation can
co-operate to
silence tumor
suppressors,
inhibition of both
DNMT and HDAC
activities can
synergize to
restore
expression of
silenced genes